"Russia murderer, go away from Syria!" chanted several dozen students who called for an end to the siege on Syria's second city, Aleppo.
The protest came as Moscow and Damascus denied claims by Ankara that the regime was responsible for an air strike that killed four Turkish soldiers last month.
A similar demonstration against Russia's backing of Assad took place on Friday, outside Istanbul University in which demonstrators called for "imperialist Russia to leave Syria".
Russia is the chief ally of the Syrian president in the conflict that has claimed more than 300,000 lives since 2011.
"Thousands of people are losing their lives," said Mehmet Akif Olgun, vice president of the National Turkish Students' Association which organised the protest, denouncing the "daily attacks" on his Muslim brothers.
In recent days, Assad's troops have pressed a fierce assault aimed at retaking the whole of Aleppo which is currently divided between regime forces in the west and rebels in the east.
But Moscow says it is not involved in the current assault on Aleppo.
Ankara is also engaged in an unprecedented operation inside Syria in support of opposition rebels against the Islamic State group but it has made no secret of the fact it wants to see Assad removed leaving it at odds with Moscow.
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